Bulk RNA-seq ITK-SYK

RNA-seq

No filtering on count matrix for TPM calculation.
Filtering only on count matrix.

Filtering

Count matrix : This count matrix was modified like followings.
B cell genes out (Cd79a, Cd79b, Jchain)
Immunoglobulin genes out
“Ighv* ,”Igl* , “Igk*

Genes like”Igf* , “Igl* (Starting with Ig- but not Immunoglobulin genes) are not removed (checked manually)


TPM table (downloadable)

PCA

PCA plot

PCA plot by condition

DEG analysis

DEG 1B vs S

DEG information table
Volcanoplot

DEG 2B vs S

DEG information table
Volcanoplot

DEG 2B vs 1B

DEG information table
Volcanoplot

ssGSEA

Single sample GSEA

Single-sample Gene Set Enrichment Analysis (ssGSEA) is an variation of the GSEA algorithm that instead of calculating enrichment scores for groups of samples (i.e Control vs Disease) and sets of genes (i.e pathways), it provides a score for each each sample and gene set pair.
(https://www.genepattern.org/modules/docs/ssGSEAProjection/4#gsc.tab=0)


ssGSEA heatmap

Color represents enrichment score


Significance by p value Heatmap

Red: p value <= 0.05 (significant)
White : p value > 0.05 (not significant)

Next work

To be discussed.